Deighan worked up the Scottish underground comics title Electric Soup in 1990, writing and drawing The Greens, a parody of The Broons strip published by D. C. Thomson. It was in working on this book that he adopted the pseudonym of Frank Quitely (a spoonerism of "quite frankly"), as he did not want his family to know it was his work, worried that they may have found it upsetting.[3]

Quitely left The Authority to draw New X-Men.[7] Quitely illustrated a Destiny story for Neil Gaiman's The Sandman: Endless Nights hardcover graphic novel in 2003.[8] After leaving New X-Men, Quitely drew the mini-series We3 in 2004, again in collaboration with Morrison.[9] He shared the 2005 Best Penciller/Inker or Penciller/Inker Team Eisner Award in a tie with artist John Cassaday for his work on the book. That same year, he and Morrison were nominated for Best Limited Series for that book, and Quitely additionally was nominated for the Best Cover Artist Eisner for both We3 and Bite Club.[10] He wrote and drew new instalments of The Greens for the Scottish underground comic Northern Lightz,[11] and in 2005 Morrison and Quitely designed a series of tarot cards for Intensive Care, an album by popstar Robbie Williams.

In December 2004, Quitely signed to a two-year exclusive contract with DC Comics, where he illustrated All-Star Superman.[12] The twelve issue series, yet another collaboration with Morrison, began publication in November 2005. Quitely and Morrison's work on the series won them the Eisner Award for Best New Series in 2006, with Quitely collecting another nomination for Best Penciller/Inker.[13] The series won Best Continuing Series in 2007 and 2009.[14] In 2008 Quitely illustrated the cover for the debut issue of Scottish underground comic Wasted.

In early 2009, Frank Quitely collaborated with the Scottish rock band The Phantom Band in designing artwork for a limited edition 7" single for their song "The Howling", which plays on Quitely's interest in occultism and esoterica. This was released as a limited run collector's pressing by Glasgow's Chemikal Underground Records.[15] That same year, Quitely again teamed with Morrison, illustrated the first three issues of Batman and Robin title,[16] which debuted in June 2009 after the "Battle for the Cowl" storyline.[17] He provided covers through issue No. 16. Quitely was one of the artists of Batman No. 700 (Aug. 2010).[18]

Quitely is the artist on Jupiter's Legacy, a ten-issue, creator-owned miniseries published by Image Comics that premiered in September 2012. It is written by Mark Millar, who described the project as "his Star Wars", and a cross between The Lord of the Rings and a large-scale superhero crossover, albeit one that will not require the in-depth knowledge normally required of such stories, as it features entirely new characters.[22]

He drew the fourth issue of Grant Morrison's The Multiversity limited series which was published in November 2014.[23][24]

^Manning, Matthew K.; Gilbert, Laura, ed. (2008). "2000s". Marvel Chronicle A Year by Year History. London, United Kingdom: Dorling Kindersley. p. 306. ISBN978-0756641238. X-Men comics...seemed to lack the innovation and creative direction that had given the team such staying power. That all changed when respected writer Grant Morrison and talented artist Frank Quitely took center stage.

^Cowsill "2000s" in Dolan, p. 324: "Grant Morrison and artist Frank Quitely unveiled one of the most original and well-received Superman series for years as they combined high-concept science-fiction elements with classic Silver Age concepts in their All Star Superman series."